LDSC_enrichment
Last updated: 2021-09-01
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Knit directory: funcFinemapping/
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| File | Version | Author | Date | Message |
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| Rmd | eaa3eee | Jing Gu | 2021-09-01 | compute standardized effect sizes |
| html | 0032b8c | Jing Gu | 2021-09-01 | Build site. |
| Rmd | 4db9eb3 | Jing Gu | 2021-09-01 | compute standardized effect sizes |
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| Rmd | bed838e | Jing Gu | 2021-09-01 | update evaluations on slicing |
Partitioned-LDSC
Technical details
HapMap3 SNPs (~1.2M): used as a proxy for well imputed SNPs and the regression SNPs in LDSC. They were generated by the international HapMap project on a collection of 1301 samples from a variaty of human populations.[https://www.sanger.ac.uk/resources/downloads/human/hapmap3.html]
Reference panel SNPs (~9M): the set of 1000G SNPs with MAF > 5% in ~500 Euproean samples
LDSC inputs/outputs:
.M/.l2.M_5_50: The .M file contains the total number of SNPs; the .l2.M_5_50 file contains the number of SNPs with minor allele frequency above 5%. By default, ldsc uses common SNPs (MAF > 5%) to estimate per SNP heritability, which is different for rare variants.
freqfile/w-ld-chr: computed on European of Phase 3 of 1kg Genomes
Regression weights: used to correct for non-independence and heteroskedasticity among the \(\chi^2\) statistics.
Regression coefficients: Quoted from the website that "They measure the additional contribution of one annotation to the model and are interpretable for both binary and continuous annotations"
- GC correction:
Baseline annotations:
DHS, H3K4me1, H3K4me3, and H3K9ac - peaks w/o flanking regions Coding, Conserved, CTCF, DGF
FANTOM5-Enhancer, Enhancer, Fetal_DHS, H3K27ac
Intron, PromoterFlanking, Promoter, Repressed, Super-enhancer, TFBS, Transcribed TSS
3-prime UTR, 5-prime UTR, Weak Enhancer
Across traits
per-standardized-annotation effect sizes
\(\tau_{c}^{*}\) is defined as the additive change in per-SNP heritability associated with a 1 s.d. increase in the value of the annotation. 
Heritability Enrichment across traits and annotations 
| Version | Author | Date |
|---|---|---|
| 0032b8c | Jing Gu | 2021-09-01 |
More details below.
\(\tau\) measures the contribution of SNPs near prioritized genes to per SNP heritability after controlling for the baseline annotations. To make \(\tau\) comparable across traits, we normalized \(\tau\) by the average per-SNP heritability for each trait and refer to this quantity as normalized \(\tau\).
sessionInfo()R version 4.0.4 (2021-02-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)
Matrix products: default
BLAS/LAPACK: /software/openblas-0.3.13-el7-x86_64/lib/libopenblas_haswellp-r0.3.13.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
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[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
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[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ggplot2_3.3.3 workflowr_1.6.2
loaded via a namespace (and not attached):
[1] Rcpp_1.0.6 highr_0.8 pillar_1.5.0 compiler_4.0.4
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[9] tools_4.0.4 digest_0.6.27 jsonlite_1.7.2 evaluate_0.14
[13] lifecycle_1.0.0 tibble_3.0.6 gtable_0.3.0 pkgconfig_2.0.3
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